org.sbml.jsbml.ontology

Class Term

java.lang.Object

org.sbml.jsbml.ontology.Term

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Term>

public class Term
extends java.lang.Object
implements java.lang.Cloneable, java.lang.Comparable<Term>, java.io.Serializable

This is a convenient wrapper class for the corresponding implementation of org.biojava3.ontology.Term in BioJava as it provides specialized methods to obtain the information from the SBO OBO file directly and under the same name as the keys are given in that file.

See Also:

org.biojava3.ontology.Term, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	def The base properties of this Term.
private java.lang.String	id The base properties of this Term.
private java.lang.String	name The base properties of this Term.
private static long	serialVersionUID Generated serial version identifier.
private org.biojava3.ontology.Term	term The underlying BioJava org.biojava3.ontology.Term.

Constructor Summary

Constructors

Constructor and Description
Term(org.biojava3.ontology.Term term) Creates a new Term instance.

Method Summary

Methods

Modifier and Type	Method and Description
Term	clone()
int	compareTo(Term term)
boolean	equals(java.lang.Object o)
java.util.Set<Term>	getChildren() Returns a set of all the children Term.
java.lang.String	getDefinition() Returns the definition of this Term, which is stored in the corresponding OBO file under the key def.
java.lang.String	getId() Returns the SBO identifier of this Term, for instance: SBO:0000031.
java.lang.String	getName() Returns the name of this Term, i.e., a very short characterization.
java.util.Set<Term>	getParentTerms() Returns the parent Terms.
Synonym[]	getSynonyms() Returns all Synonyms of this Term.
org.biojava3.ontology.Term	getTerm() Grants access to the underlying BioJava org.biojava3.ontology.Term.
boolean	isObsolete() Checks whether or not this Term is obsolete.
static java.lang.String	printTerm(Term term) Returns a String representing a term the same way as in the OBO file.
java.lang.String	toString()

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

id

private java.lang.String id

The base properties of this Term.

name

private java.lang.String name

The base properties of this Term.

def

private java.lang.String def

The base properties of this Term.

term

private org.biojava3.ontology.Term term

The underlying BioJava org.biojava3.ontology.Term.

Constructor Detail

Term

public Term(org.biojava3.ontology.Term term)

Creates a new Term instance.

Parameters:

term - a org.biojava3.ontology.Term object

Method Detail

printTerm

public static java.lang.String printTerm(Term term)

Returns a String representing a term the same way as in the OBO file.

Parameters:

term - the term to print

Returns:

a String representing a term the same way as in the OBO file.

clone

public Term clone()

Overrides:

clone in class java.lang.Object

compareTo

public int compareTo(Term term)

Specified by:

compareTo in interface java.lang.Comparable<Term>

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

getChildren

public java.util.Set<Term> getChildren()

Returns a set of all the children Term.

Returns:

a set of all the children Term.

getDefinition

public java.lang.String getDefinition()

Returns the definition of this Term, which is stored in the corresponding OBO file under the key def.

Returns:

the definition of this Term.

getId

public java.lang.String getId()

Returns the SBO identifier of this Term, for instance: SBO:0000031.

Returns:

the SBO identifier of this Term

getName

public java.lang.String getName()

Returns the name of this Term, i.e., a very short characterization.

Returns:

the name of this Term

getParentTerms

public java.util.Set<Term> getParentTerms()

Returns the parent Terms.

Returns:

the parent Terms.

getSynonyms

public Synonym[] getSynonyms()

Returns all Synonyms of this Term.

Returns:

all Synonyms of this Term. Returns an empty array if no Synonyms exist for this term, but never null.

getTerm

public org.biojava3.ontology.Term getTerm()

Grants access to the underlying BioJava org.biojava3.ontology.Term.

Returns:

the underlying BioJava org.biojava3.ontology.Term.

isObsolete

public boolean isObsolete()

Checks whether or not this Term is obsolete.

Returns:

whether or not this Term is obsolete.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object